assay-method |
extract assay data |
assayNames |
Placeholder for assay name extractor for a BQSummarizedExperiment instance. |
assayNames-method |
Placeholder for assay name extractor for a BQSummarizedExperiment instance. |
basic_clinvars |
provide a collection of basic clinical variables to limit size of clinical data return |
BQ3_Array |
create BQ3_Array instance given url (filepath) and entity (host) name |
BQ3_Array-class |
extension of DelayedArray for BigQuery content |
BQ3_ArraySeed-class |
BQ3_Array for BigQuery matrix content |
BQ3_Matrix-class |
extension of DelayedMatrix for HDF Server content |
BQ3_Source |
construct a BigQuery resource interface |
BQ3_Source-class |
a class for BigQuery tables with keys and filters baked in |
bqConn |
generate a connection to BigQuery for specific dataset |
BQM_Array |
create BQM_Array instance given url (filepath) and entity (host) name |
BQM_Array-class |
extension of DelayedArray for BigQuery content |
BQM_ArraySeed-class |
BQM_Array for BigQuery matrix content |
BQM_Matrix-class |
extension of DelayedMatrix for HDF Server content |
BQM_Source |
construct a BigQuery resource interface, for a matrix-like table with one column devoted to row identification (rowkeyfield) and all other columns assumed numeric |
BQM_Source-class |
Represent information about a BigQuery resource with a 'triple' database schema. This is targeting the isb-cgc TCGA layout. BigQuery Records are regarded as triples, within major groups defined by filtervbl. Triples have content subject - gene - value, to be pivoted to genes(rows) x subjects(columns) with values as entries. |
BQSummarizedExperiment-class |
Define a class to use BigQuery data through SummarizedExperiment interface |
cgcConn |
Simplify connection to a BigQuery dataset for the project "isb-cgc" |
DelayedArray-method |
constructor |
dim-method |
dim derived from saved dimnames |
dim-method |
dim derived from saved dimnames |
dimnames-method |
dimnames are saved in the BQ3_ArraySeed |
dimnames-method |
dimnames are saved in the BQM_ArraySeed |
goPatt |
Create a data.frame with ENSEMBL and SYMBOL identifiers associated with a GO TERM specified by a regular expression in 'termPattern' |
gtexTiss |
Convenience function for access to gene-level GTEx tissues, as quantified in recount |
isbCgcDatasets |
Access the dataset names in the "isb-cgc" project |
isbCgcTables |
List the tables in a selected dataset |
newDA |
DelayedArray bridge |
pancan_SE |
illustrate DelayedArray assay from BigQuery backend in SummarizedExperiment |
se1.3M |
Convenience functions using HSDS server to extract tenx neurons full or subset data |
seByTumor |
Given a BigQueryConnection to the 2017 GDC-oriented ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData |
seByTumor_2016 |
Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData |
tasicCortex |
A set of mouse cortex marker genes. |